--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split_libraries_illumina.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,56 @@
+<tool id="split_libraries_illumina" name="split_libraries_illumina" version="1.2.0">
+ <description>Script for processing raw Illumina Genome Analyzer II data.</description>
+ <requirements>
+  <requirement type="binary">split_libraries_illumina.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_tmpdir='$__new_file_path__'
+  split_libraries_illumina.py
+  --mapping_fp=$mapping_fp
+  --five_prime_read_fp=$five_prime_read_fp
+  --three_prime_read_fp=$three_prime_read_fp
+  --output_dir=$__new_file_path__
+  $store_unassigned
+  --quality_threshold=$quality_threshold
+  --max_bad_run_length=$max_bad_run_length
+  --min_per_read_length=$min_per_read_length
+  --sequence_max_n=$sequence_max_n
+  --start_seq_id=$start_seq_id
+  $rev_comp_barcode
+  $barcode_in_header
+ </command>
+ <inputs>
+  <param name="mapping_fp" type="data" format="tabular" label="mapping_fp"
+   help="the mapping filepath [REQUIRED]"/>
+  <param name="five_prime_read_fp" type="data" format="txt" label="five_prime_read_fp"
+   help="the 5' read filepath [default: ('NO', 'DEFAULT')]"/>
+  <param name="three_prime_read_fp" type="data" format="txt" label="three_prime_read_fp"
+   help="the 3' read filepath [default: ('NO', 'DEFAULT')]"/>
+  <param name="store_unassigned" type="boolean" truevalue="--store_unassigned" falsevalue="" checked="false" label="store_unassigned"
+   help="store seqs which can't be assigned to samples because of unknown barcodes [default: False]"/>
+  <param name="quality_threshold" type="float" value="1e-05" label="quality_threshold"
+   help="max base call error probability to consider high-quality (probability of base call being error, so values closer to 1 mean that the base call is more likely to be erroneous) [default: 1e-05]"/>
+  <param name="max_bad_run_length" type="integer" value="1" label="max_bad_run_length"
+   help="max number of consecutive low quality base calls allowed before truncating a read [default: 1; the read is trucated at thesecond low quality call]"/>
+  <param name="min_per_read_length" type="integer" value="75" label="min_per_read_length"
+   help="min number of consecutive high quality base calls to includea read (per single end read) [default: 75]"/>
+  <param name="sequence_max_n" type="integer" value="0" label="sequence_max_n"
+   help="maximum number of N characters allowed in a sequence to retain it -- this is applied after quality trimming, and is total over combined paired end reads if applicable [default: 0]"/>
+  <param name="start_seq_id" type="integer" value="0" label="start_seq_id"
+   help="start seq_ids as ascending integers beginning with start_seq_id[default: 0]"/>
+  <param name="rev_comp_barcode" type="boolean" truevalue="--rev_comp_barcode" falsevalue="" checked="false" label="rev_comp_barcode"
+   help="reverse compliment barcodes before lookup[default: False]"/>
+  <param name="barcode_in_header" type="boolean" truevalue="--barcode_in_header" falsevalue="" checked="false" label="barcode_in_header"
+   help="barcode is in header line (rather than beginning of sequence)[default: False]"/>
+ </inputs>
+ <outputs>
+  
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+